Abstract

The Epsilonproteobacteria is a class within the phylum Proteobacteria and has been primarily recognized as a group of pathogenic
microorganisms. However, nonpathogenic Epsilonproteobacteria has been increasingly of great biological importance. They represent
bacteria with the highest metabolic versatility. Nonpathogenic Epsilonproteobacteria occurs dominantly in various redoxclines
such as deep‐sea vents, stratified ocean, terrestrial sulfidic caves, and oil fields as both epi‐ or endosymbionts and free‐living
microorganisms. Recent genome analysis has revealed that some virulence determinants and the genomic plasticity of the pathogenic
Epsilonproteobacteria appear to have roots in nonpathogenic, chemoautotrophic Epsilonproteobacteria. These work advantageously
for pathogenic Epsilonproteobacteria to be efficiently and persistently infectious and for nonpathogenic Epsilonproteobacteria
to thrive in extreme habitats. In the genomic era, previously unrecognized evolutionary links are emerging between important
human/animal pathogens and their nonpathogenic, symbiotic, chemoautotrophic relatives.

Key concepts

The Epsilonproteobacteria is the class within the phylum Proteobacteria and represented by important human/animal pathogens.

The perception of the class Epsilonproteobacteria has recently changed dramatically.

Deep‐sea vents as one of the largest reservoirs of nonpathogenic Epsilonproteobacteria. Host animals (polychaete, Paralvinella; shrimp, Alvinocaris and squat crab, Shinkaia) are shown.

Figure 3.

Conservation of gene content across proteobacterial genomes in relation to phylogenetic distance. Each dot represents a pair of species within each class of Proteobacteria (96 genomes, 1126 pairs). Conservation of gene contents was calculated by dividing the number of genes shared between two genomes by the number of genes in the smaller genome. Phylogenetic distance was calculated according to Jukes–Cantor's model using the SSU rRNA gene sequences. In addition to pairs of epsilonproteobacterial species (red), pairs of endosymbionts (green) and parasites (blue) are highlighted.

Figure 4.

16S rRNA tree, with the predicted number for protein families at each node displayed (green), and the number of families gained (upper in red) or lost (lower in blue) for each branch. Some representatives of gained or lost genes are shown in parentheses. The inference of gene content was performed using the GeneTRACE algorithm (Kunin and Ouzounis, ). Protein families were assigned using the InParanoid/MultiParanoid (Remm et al., ; O'Brien et al., ). Two Deltaproteobacteria (Geobacter sulfurreducens PCA and Desulfovibrio vulgaris Hildenborough) were used as outgroup (not shown). NLG, N‐linked glycosylation system.